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Flashcards in Proteins & Enzymes Deck (91)
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1

What singular molecule makes up the primary structure of a protein? What joins these molecules together?

Amino acids are the basic unit of the primary structure of a protein, held together by peptide (covalent) bonds

2

How does the R group of an amino acid contribute to a proteins secondary structure?

It doesn't

3

What is the difference between a nucleotide and a nucleoside?

A nucleotide is a deoxyribose sugar with an attached phosphate group, while a nucleoside is a deoxyribose sugar without one

4

Draw the general chemical structure of an amino acid.

H
|
NH2--C--COOH
|
R

5

How are amino acids classified?

They are classified by the properties of their R groups

6

What type of reaction forms the peptide bond used to join amino acids together?

A hydrolysis reaction, involving the removal of a water molecule

7

Between which molecules are the hydrogen bonds formed in the secondary structure of an alpha helix?

The carbonyl- oxygen (C=O) and the amyl- hydrogen (N-H)

8

The peptide bonds in an amino acids primary sequence are rigid and planar. What do these 2 terms mean?

The peptide bonds in an amino acids primary structure are unable to rotate and all lie in the same plane

9

Explain the difference between the cis and trans conformation. Which conformation do peptide bonds exhibit?

The trans conformation involves the central carbon atom of the amino acids being on opposite sides of the peptide bond, while the cis conformation involves the central carbons being on the same side - this would cause steric clashes, and so proteins adopt the trans conformation

10

What is the isoelectric point of a protein?

The pH at which the protein has no overall net charge

11

How many amino acids are there per turn in an alpha helix?

3.6 amino acids

12

What is stronger: a parallel or anti-parallel Beta sheet?

An anti-parallel beta sheet

13

How would you define the tertiary structure of a protein?

The way in which the secondary structure of a polypeptide chain is folded or arranged into a 3-dimensional figure

14

What distance are amino acids linked by hydrogen bonds?

4 amino acids away

15

How many amino acids are there per turn in an alpha helix?

3.6 amino acids

16

What is stronger: a parallel or anti-parallel Beta sheet?

An anti-parallel beta sheet

17

How would you define the tertiary structure of a protein?

The way in which the secondary structure of a polypeptide chain is folded or arranged into a 3-dimensional figure

18

What distance are amino acids linked by hydrogen bonds?

4 amino acids away

19

What type of bond is a peptide bond?

A covalent bond

20

Amino acids contain a central carbon atom? What bond joins the amino group, carboxyl group, R group, and hydrogen atom?

Covalent bonds

21

What is an amino acid residue?

An amino acid residue is what remains after an amino acid has been incorporated into a polypeptide sequence, defined by its R group

22

What does a low pH suggest about the amount of H+ ions in solution?

There is a relatively high amount

23

What peptide bond has partial double-bond characteristics? Why is this?

A C-N bond - due to its electron resonance

24

Why don't peptide bonds exhibit cis- formation?

Due to steric clashes this configuration involves

25

Is the isoelectric point of acidic proteins greater or less than 7? What can you say about the charges of the amino acids of an acidic protein?

The isoelectric point of an acidic protein is less than 7 - the amino acids within its structure are mainly negatively charged - these amino acid tend to lose protons, giving them a negative charge, and making their external environment more H+ rich in the process

26

Is the isoelectric point of basic proteins greater or less than 7? What can you say about the charges of the amino acids of a basic protein? Why?

The isoelectric point of a basic protein is greater than 7 - the amino acids within its structure are mainly positively charged - they bind protons, giving the amino acid a positive charge, and meaning there are less protons in the external environment so it is less acidic (more basic)

27

Suggest 2 amino acid residues that are strong helix formers. Why is this?

Alanine and leucine - this is because they are small and hydrophobic

28

What is a Beta sheet?

A side-by-side arrangement of beta-strands

29

Describe the structures of fibrous and globular proteins.

- fibrous proteins are composed of long strands/sheets with a single type of recurring secondary structure
- globular proteins have a compact structure and are composed of several types of secondary structure

30

What type of protein is collagen? Describe its repeating sequence?

Collagen is a fibrous protein, and is characterised by a glycine-X-Y repeating sequence